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Sample GSM991201 Query DataSets for GSM991201
Status Public on Aug 25, 2012
Title endometrium 15 days postpartum 4
Sample type SRA
 
Source name Endometrial Biopsy
Organism Bos taurus
Characteristics time: 15 days postpartum
tissue: endometrium
breed: mixed
histological grade of inflammation: 3
Extracted molecule total RNA
Extraction protocol Frozen endometrial tissue was homogenised and total RNA was extracted using Trizol. The Illumina mRNA Sequencing Sample Preparation Kit [2009] was used to construct libraries. Poly-T oligo-attached magnetic beads allowed the isolation and pruification of poly-A tailed mRNA which was fragmented, converted to double stranded cDNA, sequencing primers and adapters were attached. 300bp fragments were then size selected for sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Data processing Base-calling done with CASAVA 1.4
mRNA-Seq reads were aligned to the Btau4.0 genome using TopHat (Settings: -r 200 --solexa1.3-quals --library-type fr-unstranded --segment-length 20 --segment-mismatches 1)
HtSeq-Count summarised the number of genes per gene (settings: mode = union)
Genome_build: Btau_4.0.62
Supplementary_files_format_and_content: Tab delimited txt files. Row 1 has ENSEMBL gene IDs and row 2 has the raw number of reads mapping to each gene.
 
Submission date Aug 23, 2012
Last update date May 15, 2019
Contact name Cathriona Foley
Organization name Teagasc
Street address Grange
City Dunsany
ZIP/Postal code Meath
Country Ireland
 
Platform ID GPL11153
Series (1)
GSE40312 Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows
Relations
SRA SRX180585
BioSample SAMN01125826

Supplementary file Size Download File type/resource
GSM991201_4_htseq.txt.gz 99.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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